RetrogeneDB ID: retro_cpor_1046

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_40:1071172..1071484(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: FAM210B
• Ensembl ID: ENSCPOG00000006630
• Aliases: None
• Description: None

Sequence

>retro_cpor_1046
TGGCTGCTGGCCTTGCTGTGCGGCCGCCGGTCCCTAGCGCTGGCCCAGTTCCAGCCCGGCCCAGACATCTGGCTGCTCCG
CGTGGTTCTCGGGGACTTCTGTGGTCACCAGGAGCCCAGCAGAATCGCTGAGACAACAGGAGACAAGGCTGCTAGCACAG
AGAACAAGCAGAGCAAGTCACAGCAGCTGAAAAGGGTTTTCCACGAACACGGAGCCGTAGGTGTGTCATTGCACGTTGGC
ATCTCACTAATCTCCCTGGACCGTTTCATGGTTGTTTCAAGTGGCGTAGACATGTCTGCAATCCTGCATAAA

Alignment

ORF - retro_cpor_1046 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.29 %
• Parental protein coverage: 56.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WLLGAATPCAPPPLALAQFRPGPDVRLLRTARRDFRSHQEPSRITETAGSKASSTESKQSKTQQLRKVFQ
          WLL..A..C....LALAQF.PGPD..LLR....DF..HQEPSRI.ET.G.KA.STE.KQSK.QQL..VF.
Retrocopy WLL--ALLCGRRSLALAQFQPGPDIWLLRVVLGDFCGHQEPSRIAETTGDKAASTENKQSKSQQLKRVFH

Parental  EYGAVAVSLHIGISLISLGLFYTVVSSGVDMSAVLLK
          E.GAV.VSLH.GISLISL..F..VVSSGVDMSA.L.K
Retrocopy EHGAVGVSLHVGISLISLDRF-MVVSSGVDMSAILHK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	2.13 RPM
SRP017611_kidney	0.00 RPM	9.95 RPM
SRP017611_liver	0.00 RPM	10.62 RPM
SRP040447_lung	0.00 RPM	8.15 RPM
SRP040447_skeletal_muscle	0.00 RPM	2.37 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1046 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1046 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006630	1 retrocopy	retro_cpor_1046 ,
Homo sapiens	ENSG00000124098	1 retrocopy	retro_hsap_653,
Nomascus leucogenys	ENSNLEG00000007028	1 retrocopy	retro_nleu_1733,
Oryctolagus cuniculus	ENSOCUG00000017897	1 retrocopy	retro_ocun_1678,
Pongo abelii	ENSPPYG00000011147	2 retrocopies	retro_pabe_577, retro_pabe_659,
Pan troglodytes	ENSPTRG00000013645	1 retrocopy	retro_ptro_475,